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<code>nextstrain update</code> behavior is user-hostile

bugSomething isn't workingSomething isn't working

Status: Open.

#457 In nextstrain/cli;

· genehack opened on Jul 17, 2025

<code>nextstrain run</code>: private pathogen repo support

Status: Open.

#449 In nextstrain/cli;

· victorlin opened on Jul 1, 2025

Bundle runtimes with pathogen repos

enhancementNew feature or requestNew feature or request

Status: Open.

#448 In nextstrain/cli;

· victorlin opened on Jul 1, 2025

[aws-batch] refresh AWS SSO session tokens

enhancementNew feature or requestNew feature or request

Status: Open.

#443 In nextstrain/cli;

· joverlee521 opened on Jun 16, 2025

<code>nextstrain update conda</code> fails when runtime has not been set up

bugSomething isn't workingSomething isn't working

Status: Open.

#440 In nextstrain/cli;

· corneliusroemer opened on Jun 4, 2025

<code>nextstrain view</code> automatic opening of browser does not work on Windows

bugSomething isn't workingSomething isn't working

source: office hoursIssue mentioned during office hoursIssue mentioned during office hours

Status: Open.

#435 In nextstrain/cli;

· victorlin opened on May 1, 2025

Bump micromamba to support new nextstrain/conda-base package

enhancementNew feature or requestNew feature or request

Status: Open.

#429 In nextstrain/cli;

· joverlee521 opened on Apr 17, 2025

[aws batch] Structured output of AWS Batch job id for programmatic use

Status: Open.

#426 In nextstrain/cli;

· tsibley opened on Mar 28, 2025

[aws batch] Overlays (e.g. <code>--augur</code>) in uploaded workdir ZIP include too much

Status: Open.

#421 In nextstrain/cli;

· tsibley opened on Mar 18, 2025

<code>nextstrain run</code>: unmanaged pathogen support?

Status: Open.

#420 In nextstrain/cli;

· tsibley opened on Mar 12, 2025

Communicate why an upload action was not allowed

enhancementNew feature or requestNew feature or request

Status: Open.

#395 In nextstrain/cli;

· jameshadfield opened on Aug 29, 2024

Update "build directory" terminology in help and docs

documentationImprovements or additions to documentationImprovements or additions to documentation

Status: Open.

#371 In nextstrain/cli;

· tsibley opened on May 29, 2024